Incursion: Alliance Effect
by Drewman784
Summary: We all remember the First Contact War, the brief but devastating contact war between the Species Alliance and the Turian Hierarchy. But now the war is over and diplomatic relations are being established as we speak. So the question is, what happens now after the war is over? *Side-story to Xcom: Incursion*
1. Chapter 1

**Hello Everyone and Welcome to Incursion: Alliance Effect! This is a side story to Xcom: Incursion so be sure to read that before reading this side story. This side story will detail the effects of Species Alliance contact with the rest of the known Galaxy, mainly the Council in the form of several short stories taking place within the time span of ten years. For the time being, me and my Beta Reader will be focusing on this sidestory. But without further ado, enjoy.**

 _ **"I may not have gone where I intended to go, but I think I have ended up where I needed to be."**_

 _ **-Douglas Adams**_

 **2110 January 7th 7:00 PM Earth Time**

 **Citadel Docking Ring**

Threielle S'iin looked out the window of the Alliance frigate, the _SAV Enlightened_ as it docked with the Citadel, watching as it carefully connected with the air lock. Threielle's mind wandered to the Citadel, searching until it found the psionic traces left by the last psionic user that visited the Citadel, years ago. Threielle knew he would be representing both the Species Alliance and the Ethereal species, not only becoming the first officially permanent Alliance ambassador on the Citadel, but the first Ethereal ambassador. One mess up could spark a major diplomatic incident-or worse. The ship jolted for a moment, signifying a successful dock with the massive station.

"Successful dock with the Citadel Ambassador, please wait for airlock pressurization." The ship's AI spoke through the speakers in a blandly polite tone.

Threielle nodded, moving to exit the ship and ushering his two sectoid assistants who carried his personal items and luggage. "Pressurization complete, you may exit the ship, Ambassador. A greeting party will be awaiting you." The AI spoke again.

"Thank you." Threielle said, having already heard of the greeting party at the briefing. With A pair of Ambassadorial guards at his side, the door slid open, floating down the ramp from the ship and onto the Citadel. The changing of brightness momentarily blinded Threielle, as the brightness inside the ship was significantly lower compared to the bright lighting inside the Citadel. Threielle spotted on the outskirts of the docking ring a large group of reporters and journalists being held at bay by several C-Sec. In front of him lay a dozen or so individuals. The greeting party composed of the three council members, Salarian, Asari, Turian. Of course the picture wouldn't be complete without the dozen or so C-sec guards present protecting the greeting party. They were only armed in light armor and with pistols, but their presence didn't go unnoticed.

"Welcome to the Citadel, Ambassador S'iin." The Asari, Tevos, said, bowing slightly towards the Ethereal. The Turian Councilor, Quentius, said nothing, instead glancing coldly at the Alliance Ambassador and nodding stiffly. The Salarian, Valern, merely looked out from his shadowed hood. Of course with but a mere look S'iin could detect their surface thoughts.

"Thank you; it is an honor to meet you all finally." S'iin said, bowing slightly and folding his four hands in front of himself, a classic Ethereal style greeting.

"If you would follow us ambassador, we have much to talk about. Sedeve and Mailyt will show your sectoids where your office and ambassadorial outpost will be." The Asari councilor said, motioning towards two Asari C-Sec guards.

"Very well." S'iin replied neutrally, psionically directing his sectoids to go with the two guards. The sectoids made the psionic equivalent of a 'yes sir', and hobbled towards the two C-Sec guards. On the outside, the two Asari stood very stiffly, not letting any emotion show, but on the inside, were growing nervous at the prospect of escorting the two sectoids, not sure of their capabilities.

"Do not worry, they are physically unfit for combat, and will not pose a threat to anyone. They are in fact harmless." S'iin said to the two Asari guards, being able to psionically sense their uncertainty. The two said Asari nervously nodded and motioned for the sectoids to follow them, their minds somewhat put to ease. The Salarian Councilor noticed this exchange and took note of it for later. As S'iin floated amongst the other Councilors, hands folded behind his back, the Salarian Councilor came up to him.

"I take it that that was psionics you just used, Ambassador S'iin?" The Salarian Councilor asked, referring to the two Asari guards. S'iin nodded.

"Yes, all of my species are very well trained in the use and applications of our psionic ability, me included. I could sense the two Asari guard's uncertainty about the sectoids. Of course, you don't need to be psionic to read faces like those." The Salarian Councilor nodded thoughtfully.

"As far as the Alliance has told us, only Humans, sectoids and Ethereals have these… psionic abilities?" S'iin made the Ethereal affirmative gesture absentmindedly.

"Yes, it is rare that a species can wield the power of psionics, much less be able to master them. The Uber Ethereal and Volunteer are to this date the only known psionic users able to truly 'master' it. Evidence of being able to control all of the Ethereal species at once, many radicals call the Uber Ethereal 'The pinnacle of evolution'." Tevos shook her head.

"No species should ever have to go through something like that, to imagine…" Tevos left off meaningfully.

"Thankfully the Uber Ethereal is now dead, in no small part due to the Humans and Zudjari. For our freedom unfortunately, we can almost never be able to repay in kind."

"Yes, this all very interesting ambassador. But if you can read our minds, how do we know whether or not you are reading ours at the moment?" Quentius inquired, still distrustful of the ambassador.

S'iin chuckled, "Simple: you do not, well it's not that simple actually. It is considered a serious offense in the Alliance to read other's minds without their consent unless in an emergency. You have nothing to fear. What I did was not reading their minds; it was more closely to examining their surface emotions, no different than say observing the body language of another. If I truly read their minds, everyone would have noticed as I exerted my will made manifest." The Ethereal's reassurances helped little as the Councilors looked at each other, worried.

The rest of the walk was uneventful save for the occasional reporter trying to get an interview with S'iin. Fortunately they were held back by C-sec who obviously had dealt with this kind of thing before in the past. As the group began to near the Council Chambers, the reporters thickened and became more apparent, following the group. Finally, S'iin held up a hand to stop the group.

"I will answer some of these reporters' questions as they are so intent on getting the answers. It would be best for the general public to get to know me better." S'iin told Tevos. Tevos nodded hesitantly and motioned for the guards to let some of the reporters through to the group. An Asari reporter holding a microphone came forward followed by a camera drone.

"Ambassador S'iin, what do you wish to accomplish here on the Citadel as the first Alliance Ambassador?" The Asari reporter said, moving the microphone to S'iin.

"Right now, the Alliance and Citadel view each other xenophobically. I wish to change that, ensuring that we can both live in peace forever without another conflict." The Asari reporter moved the microphone back to herself.

"That's a noble goal Ambassador. And I believe I speak for everyone here saying that we wish you the best of luck." S'iin nodded, and then turned his gaze back towards the rest of the reporters. Next, a Turian reporter came forward, butting his way through the crowd of reporters and holding a microphone to S'iin while another cameraman stayed behind.

"Ambassador, what are your thoughts on the Alliance's recent expansions into the Terminus Systems?" S'iin turned to the reporter, looking straight at the camera

"It is necessary to neutralize any possible threat that may arise from the Terminus area along our borders and secure it area for future colonization. That is all I have to say on the matter." The Turian reporter nodded stiffly at S'iin's short response but said nothing more.

"I believe it is time for us to move on, we only have some much time on our schedule Ambassador." Tevos said, coming up next to S'iin.

"Very well," S'iin said, turning to the reporters.

"I will answer your questions at a later date, for now I must take my leave." S'iin said to the mass of reporters, turning to depart, the flow of reporters once more blocked by C-sec. It was only another five minutes before the group reached the Council chambers and another two as everyone settled down and the negotiations actually began.

"This Council is now in session over the finalization of peace between the Turians and Alliance." Tevos stated, looking straight at S'iin who stood on the platform below, looking up at the councilors, Quentius in particular. The Turian in question locked eyes with S'iin defiantly and challenged the Ethereal to begin.

"First of all, I believe we should get the finalization of reparations underway." S'iin said, turning to Tevos and ignoring the Turian Councilor. Tevos nodded in agreement.

"Yes, that seems to be the most pressing matter. State the Species Alliance's demands, Ambassador S'iin."

"Very well, Councilors," S'iin said, pulling up his Omni tool located on his lowest left arm. The Omni tool soon flashed to life and quickly loaded the Alliance's demands.

"I am now sending the data to your own Omni tools, Councilors." S'iin started, waving the Omni tool in the general direction of all three councilors. The Omni tool made a quick chirp as it finished sending the data to the three councilors. The Salarian Councilor was the first to scan the message for any potential viruses and attempted hacks, which there were none present. Quentius inhaled sharply as he looked over the demanded amount of resources.

"Twenty five trillion credits over the course of ten years was the stated amount of credits it would take to possible repair all the physical damages before, while it is a little harsh, it is agreeable." S'iin nodded sadly.

"As I'm sure you remember my colleague Anita emphasized that the price may rise or fall. The damages were extensive to the infrastructure and personal property. More so than we initially believed, hundreds of miles of maintenance tunnels were collapsed destroying vital equipment necessary to running a young colony, combined with systematic bombardment of equipment depots for backups, and the future of Shanxi itself is put into serious doubt. This is not even entering the legal ramifications you are facing for an illegal invasion and attempted seizure of one of our worlds, and the legal battles will last for decades and the charges are in the trillions as well." Quentius glared at S'iin, clearly wanting nothing more but to strangle the Ethereal. Fortunately, Tevos stepped in before anything happened.

"Ambassador, I do have to agree with Quentius, this amount could send the Hierarchy into an economic depression." S'iin shook his head.

"Your Government has already formally agreed to pay for the rebuilding of our colony and war reparations Councilor. From the Alliance's point of view, you have no choice but to pay." Quentius' mandibles flexed rapidly, and then subsided.

Nodding his head, Quentius dismissed it, "I must speak with the Hierarchy Ambassador on this matter, and I can make no binding promises, agreements, or assurances on the matter. But I know when we've been… let off lightly." S'iin seemed to stare into the soul of the Councilor before speaking.

"I must relay to you, to back out of your promise to pay reparations Councilor… It could bring about some dire consequences." S'iin said flatly, watching the Turian's reaction closely.

"Is that a threat, ambassador?" Quentius nearly growled out, assuming a dominant stance with his hands on the podium, making him look larger than normal. "Do not test the Hierarchy's patience or resolve."

"You may perceive it however you like Councilor." S'iin stated not at all intimidated.

Quentius looked on angrily before calming down and assuming his normal position, still glaring at the ambassador.

"The last matter we have to discuss is the return of POWs, and returning the bodies of the dead." Tevos said to change the subject, as if nothing had happened.

"After the war ended, we returned both captured POWs and civilians." S'iin explained, the old Ethereals would constantly experiment with Humans and Zudjari alike. It was against the Ethereals ethical code to do such things anymore, but the Alliance did them anyway knowing full well the Ethereals did the same things decades ago. "However, some personnel were kept for testing purposes before diplomatic contact was established. I assure you most are fine, and we will return the remains of those who died in custody with a full report on them.

"You should know Ambassador that such a violation of sentient rights has dire consequences, and could void you any rights to reparations." Valern explained patiently.

S'iin nodded, "We mainly conducted noninvasive medical examinations, and through debriefings. I assure you, none were inhumanely treated, and we are grateful for that. X-Com's previous techniques are dangerous and were born of necessity; thankfully Turian soldiers are considerably less…. Single-minded. Most of our interrogations were aimed at understanding why you attacked in the first place and unlocking the Turian language. The revelations of the matter are classified, and I am currently waiting for the physical document to be transferred over so that I may show you what we found. Something most disturbing." S'iin looked to each council individually, "And I assure you, if our leading theories are correct, we may have a serious problem on all of our hands."

As soon as S'iin entered the Alliance embassy on the wards, he could already tell it wasn't going to up to par with what he had seen on the Presidium. It was in a rundown part of Tayseri ward, and the building it was housed in was very… small.

It looked rushed by any means, quickly converted to an ambassadorial quarters out of necessity. S'iin hadn't expected five star service, he would be an idiot to assume he would be given a lavish treatment after the thorough beating the Turian military and interstellar trading had suffered, combined with an almost dogmatic focus on political retaliation by the Alliance and honestly. He was amazed it had all held together for so long. The humans needed to learn some humility…

S'iin did an eerily Human like sigh and floated inside, quickly spotting his two sectoids sitting in the corner of the room. As soon as they spotted S'iin, they quickly hobbled over, standing at the end of his robes in anticipation of their next command.

S'iin felt bad for the poor sectoids, genetically modified and cloned endlessly until they became what they were now. An empty husk and mindless drone doomed to die out sooner than later. S'iin shook out of his own thoughts and closed the door behind him, instructing the sectoids psionically to bring his luggage to him so he could unpack his few belongings.

 **Jeez, sorry for not getting this out earlier guys! Me and my Beta Reader have been busy, working on three variations of the same chapter. And my Beta Reader was busy with all kinds of stuff so yeah…. So anyway, we'll be focusing on this story for around… four chapters not counting this chapter before moving onto the main story. This isn't needed to read but it would really help I believe in giving some background. Add onto the fact that schools' now in for me, I don't have much time to do anything. As a side note, sorry this chapter isn't very long but I feel I really need to get this out. On another note, don't forget to review and let me hear your thoughts!**


	2. Chapter 2

**Hey everyone and welcome back to Incursion: Alliance Effect! Last time, S'iin met the Citadel Council and set the stage for Incursion: Alliance Effect. And so now we continue with Incursion: Alliance Effect with chapter two. Sorry if this is a shorter chapter, as this is a sidestory, I want to get back to the main story (Xcom: Incursion) as soon as possible, seeing as most of the story's followers are just waiting for that to be updated. It's almost been half a year for me to update that so yeah, I would say that I should get on that as soon as possible.**

" _ **We do not remember days, we remember moments."**_

 _ **-Cesare Pavese**_

 **2110 March 12th 10:00 AM Earth Time**

 **Citadel, Alliance Embassy**

Threielle lazily opened his eyes, still drowsy from sleep. Ethereals needed more sleep than most Alliance and Council races because of the burden psionics gave to the mind, as was the norm with psionic users. Quite literally the only thing keeping his spirit within the physical form he inhabited was his considerable psionic will. Normally, Threielle would have slept in deep meditation for another hour but a loud _beeping_ sound had woken him up.

S'iin looked to his desk next to the bed and grabbed his omni-tool where the beeping was originating from. Quickly turning the Omni-tool on, he was greeted with a female synthetic voice.

"Good morning ambassador Threielle S'iin. You have one new message." The Synthetic voice said, causing S'iin to do what the Humans called "rolling one's eyes". S'iin had on occasion received messages from Alliance and Council advertisers promoting the newest in gene Therapy or Implants. 'Make Implants Great Again!' They would say. What an odd bunch. Of course they may be trying in vain to latch onto the memes of the past.

"Thank you Annabelle." S'iin said to the AI. While Annabelle wasn't a proper AI and wasn't self aware, S'iin liked to pretend that the AI could think for herself. He had adopted the trait from the other species in the Alliance, it was typical of sentient species to "Humanize" things, this served a very important evolutionary purpose, and was why humans would see faces in the weirdest of places.

"At your service ambassador." Annabelle said in a warm voice.

S'iin decided to check the message anyway, figuring it might be something actually worthwhile. S'iin began entering his twenty-three digit password, he went through his messages, quickly finding what was causing the alarm on the omni-tool to trigger. A high-priority message from the top brass in the Alliance.

Any grogginess S'iin had felt earlier was immediately wiped away as he quickly opened the message and checked its contents, making sure it was legitimate. Scrolling down the message, S'iin progressively got a sinking feeling that all was not well in the Alliance.

 **/**

 **/**

 _ **Urgent: READ AT ONCE**_

 _ **To: Ambassador Threielle S'iin**_

 _ **From: The Office of President Soule**_

 _ **Ambassador S'iin, if you have not heard of the news already, you're about to. I warn you that the contents of this message may surprise or even shock you. As of 1500 standard hours yesterday, we have been receiving reports that a small band of Batarian slavers has raided a fringe colony by the name of Fllar'r.**_

 _ **Now, we can confirm that these events have indeed transpired. Fortunately, the raiders have seemed to have underestimated the colony's ground defenses who were able to hold out until military aid could reach them. Even as the news is just coming out, the Batarian government is denying any involvement with the slavers in question, despite their reputation and the origin of nearly all the slavers were Batarian.**_

 _ **However we have some solid proof that we have extracted. This includes but is not limited to: Batarian POWs claiming their government was involved after some psionic interrogation, government documents and papers found on captured ships. There are other indicators of Batarian hegemony Involvement but we are not yet certain this isn't a False Flag operation.**_

 _ **However irrelevant of original senders, it appears our message from before has not been clearly heard. This is of course not acceptable on any level. As you know, because of the long standing political ties between the Citadel and the Hegemony, they have a permanent embassy on the Citadel.**_

 _ **As you are the only Alliance agent on the Citadel at this time, and our immediate need for information, you will need to confront the Batarian's ambassador and attempt to extract information from him. As you are reading this, your Omni-tool will be in the process of downloading a separate AI. When you approach the Batarian's ambassador, try to get as close to his computer terminal as possible so the AI can break through their firewall and into their network. While we have no indication that the Hegemony's ambassador would have any knowledge on this, he could produce some leads for us to follow up.**_

 _ **Good luck, ambassador.**_

S'iin reread the message before sighing in frustration. The Batarians knew they would be held accountable, why attack an Alliance colony? Maybe the message hadn't been clear enough in the galaxy, that it doesn't matter who you were, what your ideology was, or who you served. If you attacked the Alliance, your entire species would suffer the consequence along side you.

"Download complete." Annabelle stated matter of factly, interrupting S'iin's thought.

"Thank you Annabelle."

"Your welcome sir."

"And Annabelle?"

"Yes sir?"

"Cancel my meetings today. With apologies. I have a feeling it's going to be a long day."

"Right away Ambassador S'iin! What should I tell them?"

"If they really need me I'll be in the Hegemony Embassy Compound asking very important and uncomfortable questions."

 **2110 March 12th 10:10 AM Earth Time**

 **Citadel, Batarian Embassy**

Ambassador Gezis Kraffohan, Great Negotiator, Member of the Merchants Caste, sat at his desk in the Batarian embassy, exhausted after having to answer the questions of many angry Alliance officials complaints, demands, and outright threats to his and his species lives over his Omni-tool. Gezis was personally panicking and in deep fear. The Alliance was not someone you messed with, the Alliance brought the Hierarchy to its knees and forced the Council to negotiate at a severe disadvantage!

Even inconveniencing an Alliance Species member was asking for trouble. Outright attacking one could result in the manifestation of the Alliances threat to anyone who would dare!

The Council may have put up with it if grudgingly, but they had a reputation for not caring for something unless it directly affected the big three or if it would shake up the status quo.

But the Alliance would consider the Hegemony responsible for the crime if someone didn't come up with evidence that proved it wasn't them! No plausible deniability here. Either you were guilty or not, but it was irrelevant if you weren't guilty if you couldn't provide the information to prove your innocence.

At that moment, his Omni-tool began to vibrate, causing Gezis to power on said Omni-tool. The words _'One new message'_ quickly flashed across the screen. Gezis quickly typed in the five digit password and checked his messages.

 **/**

 **/**

 _ **Urgent: READ AT ONCE**_

 _ **To: Ambassador Gezis Kraffohan**_

 _ **From: The Office of Citadel Affairs Sovile Kraffohan**_

 _ **Brother, as you have no doubt heard, a Batarian slaving party attempted to ransack a Species Alliance colony not a Standard day ago. Reports of this… unfortunate incident have been leaked to the Alliance public and Citadel species.**_

 _ **Many high ranking officials within the Alliance are calling for a retaliation strike. Of course what the Alliance may say about us being involved is fake, you yourself know we would never hurt our friends, the Alliance.**_

' _Fat lie, we do it all the time in the Terminus'_ Gezis thought bitterly.

 _ **However with the actions of the slavers, the Alliance and many Citadel species have been angered at the Batarian Hegemony. This will almost certainly lead to violent and economic actions taken against the Hegemony. Therefore, neither we nor the Council can guarantee your safety on the Citadel either by Spectres or by an Alliance hit team of some sort. We recommend an immediate withdrawal from the Citadel, back behind the Hegemony´s border. We wish you to leave Representative Ughazon who has already volunteered to take your place in the meantime. A Batarian Military Flotilla is en route to pick you up from the Citadel docks and will meet you there in the next two standard hours. The exact coordinates are on the bottom of this message.**_

 _ **May the Pillars Grant you Wisdom and Strength brother**_

It was as he was looking at the coordinates that his Assistant came through his office door and blurred out in a worried manner, "Sire! The Alliance Representative-" The door opened to reveal the floating impassive form of Ambassador S'iin. Gezis nervously stood up from his desk.

"Ambassador S'iin, what a pleasant surprise!" S'iin floated into the room, bypassing the

assistant.

"Don't play games with me ambassador Kraffohan, you know perfectly well why I'm

here." S'iin said coldly. Gezis felt a cold shiver run up his spine.

"Ambassador, as my colleagues have stated, the Hegemony had nothing to do with the attack." S'iin shook his masked head.

"That's not where the evidence points to ambassador." Gezis' eyes looked everywhere

but at S'inn.

"I have no Idea what you're talking about." S'iin floated forward to his desk and Gezis backed up slowly.

"I think you know perfectly well what I'm talking about ambassador Kraffohan. And I can assure you ambassador, that the Hegemony will be brought to justice if our suspicions are proven correct."

"You have no right to say that ambassador." Geziz said meekly, S'iin floated closer with menace.

"And that's where you're wrong ambassador Gezis. For if your people and government are found to be guilty of wronging the people of the Alliance, ignoring the warnings we have given, you will be punished severely to make a point. And believe me when I say this; The Alliance won't take this lightly." And with that, S'iin turned abruptly and floated slowly out of the room, cape trailing behind him. Gezis shook his head and shakily sat down, the sooner he got off this damned station the better.

Gezis glanced at his computer terminal, catching a 'downloading' screen before it suddenly disappeared. Gezis looked on confused at his terminal, he had not downloaded anything, so why had there been a downloading screen? Gezis shook it off merely as an automated update of his web browser before beginning to pack for his departure from the Citadel and locking down his computer terminal and severing its connection to ensure no outside force could access it.

 **Following these events, Gezis Kraffohan would be transferred to Kharshan for debriefing and statemandated holiday, before being sent to the Batarian colony of Camala, a major population and industrial center with Eezo for negotiations with Salarians interests. Not half a standard year later, Gezis would be proclaimed dead like millions of others who tragically died on the Batarian colony of Camala in 2120 August 24th**

 _It was the beginning of the end for the Batarian Hegemony._

 _And so the Batarians and galaxy at large witness the consequences of antagonizing a dragon._

 _The Alliance Times_

 _2120 August 24th_

 _ **BATARIAN COLONY WORLD OF CAMALA ERUPTS IN FLAMES**_

 _ **Millions feared dead as a bright light of a fusion nuclear explosion rocks the colony**_

 _Batarian State National News_

 _2120 August 24th_

 _ **COLONY WORLD CAMALA ENGULFED IN EXPLOSION**_

 _ **Our beloved supreme Hegemon Khekira Drafderoh assures "Everything will be fine"**_

 _The Pillars of Truth_

 _2120 August 24th_

 _ **Colony world Camala is decimated in nuclear blast**_

 _ **Was it an accident as the authorities tell us? Or deliberate assault by jealous rivals?**_

 _Citadel Daily_

 _2120 August 25th_

 _ **Batarian Colony World Camala destroyed!**_

 _ **Millions grieve as reported deaths rises to seven million**_

 _The Alliance Times_

 _2120 September 3rd_

 _ **Death toll on Batarian colony world, Camala, rises**_

 _ **The estimated deaths have reached a new time high of 11.7 million dead according to a new report due to Eezo and radiation poisoning**_

 _Citadel Daily_

 _2120 September 11th_

 _ **The Destruction of Camala; was it an accident?**_

 _ **Rumors start circulating of a secret weapon used on the colony by Batarian Military**_

 _The Pillars of Truth [Now hunted]_

 _2120 September 13th_

 _ **Do not trust the Government!**_

 _ **They're responsible!**_

 _The Alliance Times_

 _2120 September 21st_

 _ **Protests in the Batarian Hegemony Colony of Camala Turn violent**_

 _ **Batarian Military Police reportedly opened fire into a crowd of Batarian protesters-Many feared dead; some Xeno expat and Citizens feared among executed**_

 _Batarian State National News_

 _2120 September 21st_

 _ **We urge all Batarians to come together in mourning and peace**_

 _ **Violence and protests will solve nothing**_

 _Pillars Of Truth [Underground]_

 _2120 September 26th_

 _ **Now is our time to rise up and free ourselves!**_

 _Citadel Daily_

 _2122 October 13th_

 _ **Violent riots and protests erupt across the Batarian Hegemony after documents are leaked detailing genetic testing and illegal sterilizations by the Batarian Government.**_

 _The Alliance Times_

 _2122 October 14th_

 _ **Violent takeovers across Batarian space commence conducted by what the government calls 'insurgents'.**_

 _Citadel Daily_

 _2122 October 15th_

 _ **BATARIAN HEGEMONY DECLARES MARTIAL LAW**_

 _ **The Batarian Hegemony declares martial law today, until 'insurgents' are dealt with.**_

 _ **A/N**_ **Sorry I had to leave you guys on a cliffhanger there, It will all be explained in the next chapter of Xcom: Incursion. Probably one more chapter of this and then we'll be back on track with the main story. Act II's gonna be a fun one ;) Anyway, until next time...**


	3. Chapter 3

**Hey everyone and welcome back to Xcom: Alliance Effect! This originally was going to be the next chapter in Xcom: Incursion but I decided to put this in the side story. BTW this is the last chapter of the side story so after this, make sure to keep a close eye on the main story. Also, this is my first time trying to mix media with writing as in, I'm mixing in music with my writing, and so if you see the bolded text in the middle of the writing, it's probably a song. You can usually find them on YouTube but Fanfiction has this weird thing with links so I'll just write down the name of the music. You don't have to listen to it, it's just a recommendation. Enjoy!**

" _ **A house divided against itself cannot stand."**_

 _ **-Abraham Lincoln**_

 **2123 April 9th 14:00 PM Khar'shan Time**

 _ **BHV Tunerron**_ **orbiting Khar'shan, Batarian Homeworld**

Abrephi Pacpoprak sat at his desk in his cruiser, the _BHV Tunerron_ , looking at the latest reports from the frontlines with the rebels. It had been two years since the start of the civil war, and things weren't looking good for the rebels, although they most certainly had not made it easy. According to the latest reports, they had only a handful of planets left in their control, with true Batarian forces continuously pushing back the rebels and disloyal slave scum into a corner. A chime resounded from the door, making Abrephi looked up from the reports.

"Yes? Who is it?" Abrephi called out. Pulling up his door camera.

"It is me Admiral." A harsh voice replied. Judging by the voice it sounded like Political Officer Yelcheck. Abrephi's four eyes widened as he looked at the camera, with Yelcheck looking directly at it, with a knowing look that he could see it. Of course he was the one who installed it anyways. And behind him were two of his soldiers.

Abrephi muttered as he opened the door with a single button press, Yelcheck and the two soldiers entered the room, the two soldiers, helmeted, scanned it and took flanking positions. This was not a time for being rude so Abrephi tilted his head to show subservience to Yelcheck. "Please Officer Yelcheck, take a seat." He offered politely.

"Admiral Pacpoprak, evidence has come up suggesting your brother is part of the resistance and that he has played a vital role in several rebel victories, with you passing on vital information to him. Command has demanded your presence in chains for the investigation." Abrephi looked shocked.

But he had nothing to hide; he would be proven innocent as stated under the divine pillars. Standing, walking before his desk he offered both his wrists up, "I'm assuming you will be searching this entire chamber? I assure you Officer; you'll find only evidence of my devotion to the Hegemon."

Yelcheck nodded, cuffing up his former officer and friend. "I'll be thorough. If these charges are trumped up, I'll put an end to them. The Hegemony cannot lose a fine officer such as you." Nodding to his subordinates they began to search the room. One of the soldiers pulled out a small rectangular device and began waving it around the room, stopping in front of the desk in the right corner. The soldier kneeled down, causing the device to start beeping rapidly.

"Room's bugged sir." The Batarian reported, looking for where the bug could possibly be hidden

"Strange..." Yelcheck said as he began to escort Abrephi out. "While this does paint you in a bad light, it does not indicate you are guilty, since if you were willing collaborator you could just record and report anything without a bug anyways…"

"The STG perhaps?" Abrephi suggested.

"We won't know until we retrieve the bug… but… I scan your chamber daily, how did it…" Yelcheck stiffened, "Someone may have planted it specifically to implicate you. Of course they didn't think out that I took my job seriously." Yelcheck said to himself.

"Wait you search my chambers daily?" Abrephi asked in surprise.

"Alert, alert, unscheduled relay activation. Rebel ships exiting from the mass relay." The familiar voice of Abrephi's XO reported in.

"What? How's that possible? How would any rebel ships get past the outer pickets and Verge Relay wall?" Yelcheck said to himself in alarm, as everyone stopped to think themselves. And the possibility of a Rebel fleet somehow evading or destroying the large parts of the Batarian Navy guarding the route to Khar'shan was inconceivable, and if they had gotten through through blind luck or skill, heads would roll.

"This isn't good, somethings up..." The flaking soldiers both nodded in agreement, this was not something to take lightly.

"Come on then, let's go." Yelcheck said, motioning for the group to move on. The two soldiers took the arms of Abrephi to ensure that he didn't escape, even if it was ultimately unnecessary. A minute of walking down the halls passed before Yelcheck slowed his pace.

It was soon explained with sudden and extremely loud warning klaxons, "ALARM, ALARM: SPECIES ALLIANCE VESSELS DETECTED! THIS IS NOT A DRILL, REPEAT, THIS IS NOT A DRILL."

Yelcheck pressed his comm closer and looked drained, "The comms are being flooded, and their saying the Alliance is here, helping the rebels!" Yelcheck explained, trying his best to keep calm knowing all too well that an Alliance intervention on the rebel's behalf would spell a crushing rebel victory, and above the Homeworld no less would mean a certain Rebel victory for the war. The ship's' speakers crackled to life with a smooth voice.

" _Attention all Batarian Hegemony vessels in system, this is Admiral Kilby Lecates of the SAV Vengeance. Surrender and deactivate all systems now or face complete annihilation. Let the wreckages of your comrades by the relay stand as testament of our true strength. You have exactly five minutes to comply. If any Batarian ship fires upon our fleet, we will respond in kind."_ Yelcheck cursed.

"High command is going to have a panic over this." Yelcheck said, turning to the rest of the group.

"We need to get out of here, the defenses won't hold, not against Alliance ships." Abrephi continued, looking at Yelcheck. "This fight won't even be categorized as a battle to them."

"We can't, the Alliance and rebels are blocking the relay, and even if that was possible they could just outrun us, for all we know this is just one part of a general offensive across the entire Hegemony." Yelcheck speculated, cursing.

"I'll try and get ahold of the grand admiral, try to convince him to lower arms." The likelihood of success was nil, the bastard was too stubborn and prideful to surrender. Yelcheck leaned his back against his wall and muttered into his earpiece for several minutes before cursing more colorfully.

"The damned fool would rather die than to surrender and face humiliation. They also said that if we deactivated our weapons like the Alliance asked, 'loyal' Batarian ships would fire on us."

"What do we do now?" Abrephi muttered to himself.

"There's no way out of this one I'm afraid old friend." Yelcheck said, patting Abrephi on the back.

Ideas were formulating in his mind, "What about the escape pods? We could scuttle the ship and have the crew escape the ship through them and wait out the destruction in there. We should also announce this to other ships, to deny the rebels the honor of facing us in combat." Abrephi suggested, a smile on his face.

Yelcheck looked thoughtful, this was not the first time Abrephi has come up with an unorthodox idea like this, "The Alliance could just shoot us down." The soldier on the left put in. The soldier on the right elbowed the other soldier and gave him a look telling him to shut up.

"It's better to have a chance out there than no chance in here." Yelcheck said. Abrephi nodded. "Captain, I believe you should have the honor of giving one last speech to the crew."

Removing the cuffs around his wrists, Abrephi prepare himself to speak through his earpiece.

"Loyal Batarians of the Hegemony." Abrephi started, clearing his throat. "We are surrounded, outgunned and outnumbered by the Alliance ships, in other words we have no chance of surviving if we chose to fight. So it is with a heavy heart I propose another option. All crew are to evacuate to the escape pods, and live to serve the Hegemony another day. Some of us will die, but by the pillars, not all of us. Commander Zalche, when the crew is away plot a FTL path to the nearest Alliance cruisers, I'd like to give the girl one last victory. That is all." Immediately, the comms erupted in shouting voices and Abrephi turned the comms off, nodding to Yelcheck.

 **-XCOM 2 Soundtrack: Combat Music 1 - Extended-**

" _Attention all Batarian combatants, your time is up,"_ The ship's speakers crackled. " _Surrender now, be informed that any false surrenders will be met with harsh judicial punishment…. And vivisections."_ The speakers died, leaving only the hum of the engines to hear. Yelcheck turned into the comms only to wince and turn the comms off.

"We need to go; we have not a moment to lose." Abrephi stated, glancing at Yelcheck.

"Agreed." Yelcheck said. The group had only started towards the escape pods when the ship shook suddenly, causing some crew in the halls to lose their balance.

"What in the pillars was that?" Yelcheck cursed. The ship's speakers crackled to life once more.

"Attention all personal, Hostile forces are launching boarding torpedoes. I repeat, hostile forces are launching boarding torpedoes. Point defense crews, if one of those torpedoes gets through, the ship is lost like our dear captain said, if we are boarded all crew is to evacuate immediately." Zalche announced.

¨Just perfect! I guess your call was correct, best to get to the escape pods." Yelcheck hissed, motioning for the others to follow him as they began making their way to the escape pods on their side of the ship.

Since they had not been boarded yet, thanks mostly to the fact the ship itself was situated in the center of the fleet, the crewmen they passed were all moving in the same direction to the escape pods. However, destruction or boarding was inevitable, and likely soon, as Yelcheck checked his omnitool, the solar map showed a lot less Batarian ships than when they started.

They were almost to the escape pods when the ship rocked badly, as if impacted by something that massed at least half the ship, "All crew evacuate immediately, engineering, initiate self-destruct! Security, contain and delay for the crew." The other crewmen around their captain and political officer looked worried, but produced their service sidearms.

"Come on, we gotta go." Yelcheck said, as he started to lead the group of crew men which was rapidly growing as now the essential service personnel joined them in their rush to the escape pods. Numbering at over a dozen they reached the next junction only to be confronted with a security team.

"Come on, that door won't hold up forever!" The Arms Men shouted as he and his men prepared how they could, many of them covered in ash and blood. Looking to the Admiral and his group he raised his hand for halt. An even louder bang was heard, and the door he was talking about was nearly ripped off its mountings. "Shit, prepare grenades, and get that HMG ready, as soon as that door buckles, let them have it!"

As the Crewmen started to sprint past to get across the junction to the escape pods past it, half the group got by when the door was finally ripped apart, and the entry way was flooded with both bodies and gunfire. The borders closely resembled some smaller arthropod species on Khar'shan, except these… looked almost evil in a way. Their armored exoskeleton was purple, with spike like appendages covering their spiny legs, head, and short clawed arms. Their glowing yellow eyes seemed to stare into the souls of the four Batarians, who were unmoving and transfixed on the… demons. Only for a moment were they intimidating before they were all shredded by the heavy machine gun and the half dozen rifles, and nearly a dozen pistols fired at them. Hardly a few got more than few meters before the last one collapsed from its wounds.

"Come, we have to go!" Yelcheck roared, grabbing Abrephi by the collar of his uniform and pulling the Batarian with him. This seemed to break the spell on the other naval crewmen as they started to follow as soon the hole that was a door started to shoot back with green plasma, which hit an Armsman evaporating his upper body, and started up the suppressing fire once more.

"Almost there, come on! I never thought I'd see a Chrysalid and live to tell about it." Yelcheck shouted, the fighting behind the Batarians either ending or growing too distant. Everyone was knocked off their feet as something outside impacted the ship, warning klaxons and preprogrammed announcements came on.

Everyone picked themselves up or were helped off by their more intact comrades, Abrephi took a moment to close the bulkhead behind them, if any other crewmen came this way they could open it, and it would slow down the borders.

After what felt like an eternity of running, but was actually hardly a minute, they reached the escape pod deck. The sound of people screaming orders, and pod chiefs giving orders was deafening, the klaxons and Zelche giving announcements simply adding more noise. Already a quarter of the escape pods were launched, and as more filled up, they were launched.

"Get in; once the pod is filled to capacity, launch the pod, there's enough for everyone so don't worry about seats!" One of the crew chiefs was screaming as he stood in his pulpit, secured with a few safety lines.

"This way." Yelcheck motioned, nearly dragging Abrephi to the nearest pod with enough seats, using his executive powers to jump the cue at it. "Here." Yelcheck announced, pushing and then securing Abrephi into place in the pod. The pod was almost full and Yelcheck took his seat while he could, while not right next to his commander he was at least in the same pod.

Scant seconds later the pod was filled up and the door shut after the crew chief for the pod checked everyone's fastenings. After a few moments of movement into launch position, the pod stopped momentarily and then suddenly the feeling of thrusters and vertigo kicked in, and the pod was blasted from the ship as quickly as it could go, the VI autopilot taking them on a safe route away from the ship and any potential debris.

From the door porthole, the ship grew ever smaller, but Abrephi's keen eyes could spot the boarding torpedo hits, and the other pods launching from the ship. Looking at what the rest of the space surrounding Khar'shan he could, it was a massacre. Any Batarian ship that attempted to fire on the advancing Alliance fleet was being torn to shreds, debris the only reminder anything was ever there.

As the _Tunerron_ advanced towards the nearest Alliance ship, quickly distancing so that it could not be viewed with the naked eye, Abrephi brought up his Omni-tool. His link to the ship was still solid, and he could see a real time model of it as it was peppered with plasma and laser fire, shredding entire compartments of the ship as the enemy apparently figuring out what Abrephi's plan was. The Alliance began maneuvering their own ships out of the way and began bombarding the ship with weapon fire aiming to destroy the engines, boarding and escape pods lifting off from the ship as the Batarian ship as it neared its destination, an outlying Alliance cruiser.

Unfortunately for the cruiser, it was simply too slow to react, having been committed to entering geosynchronous orbit with Khar'shan, the Batarian ship going full speed towards the alliance ship. Even as chunks of the hull and armor were blown away from the ship, it somehow retained its basic shape.

Abrephi watched in pride as the ship finally reported all escape pods launched, and the Batarian ship entering lightspeed and instantly impacting the Alliance vessel. By the time the dust cleared nothing was left of either ship, as the Batarian ship had only reached 1.8 _C_. But this hardly had an impact on the greater battle, as he found that almost no Alliance ship had been actually destroyed to such a degree, and only a large part of the Rebel ships had been even damaged or knocked out of action. Several minutes after the destruction of the _Tunerron_ , the only ships left were Alliance, surrendered or disabled Batarian ships, and an almost shocking level of Batarian escape pods among the system.

After an hour silence of making their way to Khar'shan to crash land safely on the planet surface, the crew chief shouted out, pointing at the porthole. You could barely make it out, a speck in the blackness of space. But it was approaching the pod, a black capsule about half the size of the escape pod they themselves were in. As the object got closer, Abrephi could make out an Alliance insignia on the side of the pod like object.

Within a matter of seconds, the capsule was there, and with a hiss, locked with the escape pod. This was the end, as the pod started to accelerate to the closest Alliance vessel he realized it was an automated retrieval tug for escape pods. The Alliance was being thorough in their cleanup, and they likely didn't want any Batarian naval personnel on the planet if they could help it. He had to give them that they were efficient in their plans, while his ship could most certainly do nothing to fight the alliance's superior weapons, as a ground commander he would have been much more effective..

For several moments, nothing happened, sixty eyes focused on the peculiar machine as they were carried along to a frigate. Without warning, the machine hummed loudly, startling the Batarians. And as soon as he realized it they had been attached to an airlock on the vessel. They had no time to prepare, as a puff of bluish smoke expelled from the entrance and quickly envelop the pod.

With no time to put on hardsuits or even breath masks, the Batarian occupants were soon knocked unconscious by the gas as it permeated their porous skin or entered their lungs. The last thing Abrephi saw before his vision went black was the door opening...

 **A/N: And that wraps up the last chapter for this sidestory, next I will be focusing on the main story. Since most of my readers are probably still waiting for that to be updated without knowing this side story is a thing… yeah sorry guys. Anyway, I'll be going on vacation this Christmas, meet with the family and all that bizz. So yeah, happy holidays to all of you guys out there! See you all next chapter. And before I forget, don't forget to leave a review so I can better my writing, my work lives off of your guy's devotion to this story!**


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